Admittedly, I have little data, but it seems as if iTunes 12.3 and iOS 9 have combined to not lose my iPhone from the device listings. Whenever I've tried to do a WiFi sync, it's worked. That's an improvement.

"Design is not just what it looks like and feels like. Design is how it works."
Steve Jobs

Actually, the problems continue, but are far less frequent and less problematic than before.
To recap, roundabout iOS 8, WiFi syncing got flakey. My iPhone 6 would drop out of the Devices list in iTunes. My iPad 4 never did. I could get the iPhone 6 back on board with an iPhone restart or by plugging it in, or by restarting iTunes. Occasionally the iPhone 6 just reappeared for no reason I could detect.

iOS 9 and the concurrent iTunes versions seem to have mostly, but not completely fixed that issue with my iPhone 6s. Since I got my iPad Pro last week, it has occasionally dropped out of the iTunes Devices list. Strangely, just waking the screen brings it back. Today I saw the same issue with my iPhone 6s. I started a sync and the iPhone just disappeared from the Devices list. I clicked the Home button and it reappeared.

"Design is not just what it looks like and feels like. Design is how it works."
Steve Jobs